Identifying fungal-specific aspects in ribosome production as new targets for anti-fungal drugs

Keywords: Human and plant pathogens, Health, Antimicrobial resistance, Food safety
The production of ribosomes, large RNA-protein machineries that synthesise all cellular proteins, directly determines the proliferative rate of cells or unicellular organisms. Defects in ribosomal RNA processing are linked to many inherited human diseases ("ribosomopathies") and several cancers.
Key events in ribosomal RNA maturation are endonucleolytic cleavages that release the mature ribosomal RNAs from a precursor transcript, but many of the enzymes are surprisingly still unknown. The eukaryotic ribosome biogenesis pathway was originally characterised and initially almost exclusively studied in budding yeast (Saccharomyces cerevisiae), but predicted orthologues of most yeast biogenesis factors are also present in other fungi and higher eukaryotes.
Recent studies in the mammalian system have revealed that the usage of two critical cleavage sites and at least one corresponding endonuclease are different from yeast. This finding suggests that several major aspects of human ribosome biogenesis might be different to those seen in all fungi. Therefore, the fungal-specific elements would be excellent targets for new therapeutic strategies against pathogenic fungi. However, studies of ribosome maturation in model pathogenic fungi are currently almost non-existent.
To identify truly fungal-specific endonucleases and cleavage events in ribosome biogenesis, this PhD project will therefore involve comparative analyses in different fungal species. The research will be carried out in budding yeast and in the model and pathogenic fungi, Aspergillus nidulans and Candida albicans, respectively, taking advantage of their sequenced genomes and established laboratory protocols.
Aspergillus fumigatus, a closely related member of the Aspergillus genus, and Candida albicans are both major human pathogens that affect individuals with compromised immune systems, including chemotherapy patientsand lung disorders, which have significant health and socioeconomic implications, particularly in ageing populations . Research outcomes in Aspergillus nidulans will also be transferrable onto plant fungal pathogens within (and related to) the Aspergillus genus that cause disease on grain crops and synthesize mycotoxins, which can contaminate food. 25% of world food crops are affected and the financial loss to farming caused by mycotoxins is alarming.
During the project, the student will acquire expertise in bioinformatics, genetics, molecular biology and biochemical techniques, taking advantage of leading-edge RNA-protein crosslinking techniques and next generation sequencing.
The student will first apply in vitro and in vivo approaches to identify and characterise fungal-specific enzymes. One very promising candidate for a fungal-specific endonuclease is RNase MRP, which cleaves yeast pre-ribosomal RNA at one specific site, while human RNase MRP is not involved in ribosome biogenesis. The role of RNase MRP and other candidate enzyme in model pathogenic fungi will be studied.
In addition, the student will also establish a system to specifically block cleavage at several mapped pre-ribosomal RNA sites in budding yeast, which is expected to strongly affect survival. This approach will determine the importance of individual cleavage events under different growth conditions and can, if successful, be adapted to specifically inhibit growth of pathogenic fungi.
Outcomes of this work will provide new angles for the design of specific chemical inhibitors that can be used to modulate and further understand the key features of a fundamentally important cellular pathway. Given the increasing problem of fungal multi-drug resistance, the predicted identification of new targets for drug design will be beneficial for food production and human healthcare .